Second mode disturbances dominate the primary instability stage of transition in a number of hypersonic flow configurations. The highest amplification rates of second mode disturbances are usually associated with 2D (or axisymmetric) perturbations and, therefore, a likely scenario for the onset of the three-dimensionality required for laminar-turbulent transition corresponds to the parametric amplification of 3D secondary instabilities in the presence of 2D, finite amplitude second mode disturbances. The secondary instability of second mode disturbances is studied for selected canonical flow configurations. The basic state for the secondary instability analysis is obtained by tracking the linear and nonlinear evolution of 2D, second mode disturbances using nonlinear parabolized stability equations. Unlike in previous studies, the selection of primary disturbances used for the secondary instability analysis was based on their potential relevance to transition in a low disturbance environment and the effects of nonlinearity on the evolution of primary disturbances was accounted for. Strongly nonlinear effects related to the self-interaction of second mode disturbances lead to an upstream shift in the upper branch neutral location. Secondary instability computations confirm the previously known dominance of subharmonic modes at relatively small primary amplitudes. However, for the Purdue Mach 6 compression cone configuration, it was shown that a strong fundamental secondary instability can exist for a range of initial amplitudes of the most amplified second mode disturbance, indicating that the exclusive focus on subharmonic modes in the previous applications of secondary instability theory to second mode primary instability may not have been fully justified.